For example, I have two proteins from two different families. To estimate if some species have them both I would run two rounds of blast and see.
But what If I have not only one species but three hundred, how to automize this search? As output, I want to get a list of species and for each species information about the existence of each protein in this species. I work with bacteria and this co-occurrence can be a signal of interactions between these proteins. Additionally, I don't want to see co-occurrence of these proteins in every bacteria, I want to estimate what percent of bacteria that have the first protein has the second protein.
Sorry for the simple questions, I'm new in this field, and sometimes it's very hard to find the point to start. Thanks in advance)